DNA extraction replicates improve diversity and compositional dissimilarity in metabarcoding of eukaryotes in marine sediments

Environmental Sequencing Provides Reasonable Estimates of the Relative Abundance of Specific Picoeukaryotes

(2016) Caterina R. Giner et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling

(2016) Rosalinda D’Amore et al.   BMC GENOMICS

High-throughput metabarcoding of eukaryotic diversity for environmental monitoring of offshore oil-drilling activities

(2016) Anders Lanzén et al.   MOLECULAR ECOLOGY

Indexed PCR Primers Induce Template-Specific Bias in Large-Scale DNA Sequencing Studies

(2016) James L. O’Donnell et al.   PLoS One

Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons

(2016) C. Ryan Penton et al.   Frontiers in Microbiology

A comparison of DNA extraction methods for biodiversity studies of eukaryotes in marine sediments

(2015) K Lekang et al.   AQUATIC MICROBIAL ECOLOGY

How will the ‘molecular revolution’ contribute to biological recording?

(2015) Lori Lawson Handley   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Meiofaunal community analysis by high-throughput sequencing: Comparison of extraction, quality filtering, and clustering methods

(2015) Pamela M. Brannock et al.   Marine Genomics

Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities?

(2015) Emily A. Brown et al.   Ecology and Evolution

Metabarcoding Is Powerful yet Still Blind: A Comparative Analysis of Morphological and Molecular Surveys of Seagrass Communities

(2015) Dominique A. Cowart et al.   PLoS One

Deep-Sea, Deep-Sequencing: Metabarcoding Extracellular DNA from Sediments of Marine Canyons

(2015) Magdalena Guardiola et al.   PLoS One

Patchiness of deep-sea benthic Foraminifera across the Southern Ocean: Insights from high-throughput DNA sequencing

(2014) Franck Lejzerowicz et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

A molecular-based approach for examining responses of eukaryotes in microcosms to contaminant-spiked estuarine sediments

(2014) Anthony A. Chariton et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data

(2014) Gentile F. Ficetola et al.   Molecular Ecology Resources

Sequence Depth, Not PCR Replication, Improves Ecological Inference from Next Generation DNA Sequencing

(2014) Dylan P. Smith et al.   PLoS One

Characterization of the 18S rRNA Gene for Designing Universal Eukaryote Specific Primers

(2014) Kenan Hadziavdic et al.   PLoS One

Challenging the paradigms of deep-sea ecology

(2014) Roberto Danovaro et al.   TRENDS IN ECOLOGY & EVOLUTION

Multiple spatial scale analyses provide new clues on patterns and drivers of deep-sea nematode diversity

(2013) Roberto Danovaro et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Marine monitoring during an economic crisis: The cure is worse than the disease

(2013) Ángel Borja et al.   MARINE POLLUTION BULLETIN

Genomics in marine monitoring: New opportunities for assessing marine health status

(2013) Sarah J. Bourlat et al.   MARINE POLLUTION BULLETIN

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Extremely High Copy Numbers and Polymorphisms of the rDNA Operon Estimated from Single Cell Analysis of Oligotrich and Peritrich Ciliates

(2013) Jun Gong et al.   PROTIST

Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing

(2012) DONALD J. BAIRD et al.   MOLECULAR ECOLOGY

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Dramatic Shifts in Benthic Microbial Eukaryote Communities following the Deepwater Horizon Oil Spill

(2012) Holly M. Bik et al.   PLoS One

Testing the Limits of 454 Pyrotag Sequencing: Reproducibility, Quantitative Assessment and Comparison to T-RFLP Fingerprinting of Aquifer Microbes

(2012) Giovanni Pilloni et al.   PLoS One

CREST – Classification Resources for Environmental Sequence Tags

(2012) Anders Lanzén et al.   PLoS One

Sequencing our way towards understanding global eukaryotic biodiversity

(2012) Holly M. Bik et al.   TRENDS IN ECOLOGY & EVOLUTION

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

Man and the Last Great Wilderness: Human Impact on the Deep Sea

(2011) Eva Ramirez-Llodra et al.   PLoS One

Replicate or lie

(2010) James I. Prosser   ENVIRONMENTAL MICROBIOLOGY

Assessment of Bias Associated with Incomplete Extraction of Microbial DNA from Soil

(2009) L. M. Feinstein et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Quantification of the Detrimental Effect of a Single Primer-Template Mismatch by Real-Time PCR Using the 16S rRNA Gene as an Example

(2008) D. Bru et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Quantification of Diatom and Dinoflagellate Biomasses in Coastal Marine Seawater Samples by Real-Time PCR

(2008) A. Godhe et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea

(2008) Z. M.-P. Lee et al.   NUCLEIC ACIDS RESEARCH